


The Silent Song

by eatsleepwritespoilers



Category: Doctor Who, Doctor Who (2005)
Genre: Angst, Eleventh Doctor Era, Family, Gen, Mystery, Post Season/Series 06
Language: English
Status: In-Progress
Published: 2013-06-13
Updated: 2013-06-14
Packaged: 2017-12-14 22:06:55
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 8
Words: 8,778
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/841893
Author URL: https://archiveofourown.org/users/eatsleepwritespoilers/pseuds/eatsleepwritespoilers
Summary: <blockquote class="userstuff">
              <p>Set after season 6. The Doctor just wants to spend time with his wife River, but shenanigans get in the way as a young ginger girl runs into the Tardis bringing along an adventure the Doctor can't refuse. She knows him but he has never seen her in his life. Emilie Smith is a mystery worth solving. With the help of Amy, Rory and River they try to figure out who this girl is and why she is in danger.</p>
            </blockquote>





	1. The Beginning of the End

**Author's Note:**

> Hi everyone! I am so excited to be publishing my first (and hopefully not my last) Doctor Who Fanfiction! It's been a while since I published anything on this site and the last thing was Twilight which was...a really long time ago! Hopefully my writing and storytelling has improved since then ;) Now some ground rules and knowledge before we begin:
> 
> This story takes place in between Season's 6 and 7 and is a canon story. I don't want to reveal any more information and will just let you get to the story!
> 
> I would like to give a HUGE THANK YOU to my lovely Beta goblindreamer who has made this story more pleasing to the grammar eye :)
> 
> Now onto the first chapter! *cue theme song*

Chapter One: The Beginning of the End

In the middle of Lake Silencio, the fire burned high into the sky. The cloudless night made the flames brighter, making fire noticeable for miles. Some would see the flames from the roads and assume some teenagers were making another bonfire by the lake, while others who were closer could see the fire was in the center of the lake. To the average person walking by, it looked like the cover of a murder like from the movies. In truth that's exactly what it was, but of course there was more to the story than just the fire in the middle of the lake.

This fire in the middle of the lake was burning the body of one of the greatest men the universe has ever known. The man floating in the burning boat has seen the beginning and end of the universe and everything in between. He has saved the world more times than any one person could know and never been thanked once. He never asked for thanks though; he did all of this because he wanted to. He risked his life all because he loved the universe and the secrets it held with it and would do anything to protect it.

But in one moment, he stood at the edge of the lake, in front of his friends who were his family and was shot by the women he loved. His friends watched as he fell to the ground shot in the middle of his regeneration process. They watched as the man who they loved deeply die. They now knew he asked them to be there so he wouldn't die alone. But that was hours ago, and now the only thing left was the boat floating in the middle of the lake as the body of the man they loved burned into the night sky.

Over on the other side of the rocks, the Doctor watched his body burn until there was nothing left. He watched, knowing everything he has worked for in the past thousand years of life turn to ash. After all, the man burning in the boat really wasn't the Doctor, just a robot filled with tiny people and his tiny self. See time told him he had to be here; not that he had to die. So he asked the Teselecta people to help him this one last time. The Doctor watched the sky grow darker and knew by now he would have flown away in the Tardis leaving the robot and the people inside left in the ship. He looked down at his watch knowing it was time to go retrieve the body and make sure the people inside were really okay.

The Doctor brought the robot on shore, afraid to look down and see himself. He knew it was silly, but the thought of seeing his body dead only scared him a bit. The Teselecta though already went into emergency auto and was just a plain robot, silver and shiny. Not a burn was in sight except for a couple of golden marks on the edges. One eye began to open and glowed bright until a young man was standing in front of the Doctor.

"Thank you again for saving me Captain and sorry about the timeline change there. I didn't know River would do that." The Doctor said, putting his hand out and shaking the Teselecta Captains' hand.

"The pleasure was ours, Doctor. Now that we know the truth of the events that happened tonight, we would be happy to erase the data on your wife River Songs' The Captain began to explain how knowing that River was forced into committing the murder made the tesselect people feel that she wouldn't be a threat to the rest of the world. The Doctor though stopped listening once he heard "wife". Hearing River being called his wife for the first time suddenly made it seem like the mystery behind River Song was solved. There was no more need for the secrets between them.

"You know, can you keep the records? Fixed points in time and all, I don't want to mess with fate."

"Of course. We understand."

The men talked a bit more about business including on how to act now that the Doctor was "dead". After reaching a conclusion on the matter the Captain put his hand out and shook the Doctors hand.

"Well, we must be on our way, Doctor." The Captain finished the conversation by saluting the Doctor and turning back to the laying Teselecta Robot. The bright light came again taking the Captain back to his ship.

The Doctor turned away to see his Tardis standing off into the distance. The blue police box was waiting for him, ready to travel the universe; the only question was where to? He was free of the Silence once and for all. Everyone he knew assumed he was deadexcept the Ponds. They were very upset with him knowing he kept it a secret from them but he made amends after Christmas, and they couldn't stay mad at him forever.

He entered his Tardis and began to enter coordinates to a planet where his favorite restaurant resided. It was a beautiful planet with the best fish fingers and custard he ever tasted. As the Tardis reached his destination, he received an urgent message from his physic paper reading "Hello Sweetie" attached with coordinates.

River Song, he would never stop saving his new wife. He still couldn't get over her new title. Of course, he always knew that she was his wife but he assumed it was by force. Now he knows he did it because he really loved her. If he had to do everything over again, he would have made a proper ceremony of things, but time was of the essence in that reality so the quick version was all he could do.

He rolled his eyes thinking of River and knowing this would be the first time he would see her after she "killed" him. He flew the Tardis to his new destination and quickly opened the door knowing she would be standing waiting for him like she always was.

Only this time, it wasn't River Song.

He saw the figure of a redheaded girl running straight for the Tardis. She was obviously running from something and knew he would be there to save her, but how? He didn't have time to ponder though as the girl ran straight into the Tardis. The young girl flinged her jacket on the coat rack and advanced up to the control room. She was yelling at no one in particular but everyone at once. Not noticing the Timelord was still at the open door. He quickly closed the door and walked up to see that she had taken a seat in one of the chairs. Questions were buzzing around in his head but they would all have to wait. The girl suddenly interrupted his thoughts by turning to him yelling "Allons-y!"


	2. The Girl in the Tardis

**Summary for the Chapter:**

> Questions need to be answered as the Doctor is suspicious of the Ginger girl.

Chapter 2: The Girl in the Tardis

The young girl sat staring at the Doctor. She had never seen him look like this before in her life, so shocked by her presence. Of course, he sometimes looked surprised that she would show up suddenly but he was at least happy to see her. Never so shocked.

"Aren't we going?" She said slowly to him as if she was speaking to a child. He was never this slow before. It's not like she did anything different this time either. She just jumped into the Tardis like she always did. Then, he would walk over and ask her where she wanted to go and would take her where she wanted or sometimes it would be a surprise; somewhere she had never heard before.

"Going where wait; who are you?" She could see the anger build up in him but what for?

All of the sudden hit her. He didn't know who she was. This version of the Doctor had no idea who she was. Not one adventure, story, or-. She had to stop thinking like this. The girl quickly composed herself long enough to stand up and put out her hand.

"Emilie…Smith, nice to meet you Doctor." She instantly regretted the name as soon as it came out of her mouth.Great job Em, nice job being quick on your feet there.She thought to herself. Okay, really though, Smith wasn't the best last name to pick…If only he figured it out; but he didn't

"Well Emilie, how did you know about the Tardis? How did you know you could contact me with that saying? I mean I thought I would be getting-" He was getting flustered and more angry so she had to stop him before it got dangerous.

"River?" She cut him off softly before he asked any more questions. The name instantly calmed him down. Of course he would expect River. Emilie had forgotten the catchphrase use to belong to a single person until now.

"Yes. River… How do you know her exactly?" He asked, a bit calmer this time crossing his arms in front of his chest.

"Well, River and I met at the University. She used to tell me stories about the Doctor and how she could contact him at will. She told me how I could reach you if I was ever in trouble." Emilie rambled on hoping he would stop her, but he never did. He just stood there listening.Well, at least this was making more sense, he thought, she knew River. But things still weren't adding up in his mind.

"Trouble. Okay, I'm good with trouble or problems, so what is it?" He asked her.

Emilie opened her mouth to respond when she suddenly couldn't remember. What happened? She was in the middle of the forest with…? When all of the sudden…nothing. She couldn't seem to remember anything from the event, just that she knew she had to run.

"I don't know. I can't remember." She raised her hands to her forehead when all of the sudden the Doctor grabbed her arm.

"What are those?" He asked her suddenly examining her arm. Emilie looked down on her arm and saw 4 black hash marks on her wrist. "I don't know. I didn't put those there." She replied defensively snatching her arm from his grasp. What were those markings? Emilie had never seen them in her life and she knew she didn't put them there, so who did?

"Emilie run." He suddenly grabbed her wrist, drawing something, before pointing her in a direction.

"I will be at the end of the forest Em. Don't forget." Looking at her one last time before…

The flashback ended. She was remembering bits and pieces but not the whole story. So at least she knew that he was there. He must have been the one to mark her arm. Well, that made her feel more comfortable but, she still wondered why. Why would he put slash marks on her arm unless he was trying to leave a message for himself?

His past version.

The Doctor just stared at her, suddenly becoming more serious.

"Emilie, what do you remember? Why were you there?"

"I don't remember." She was getting agitated from all the was time for her to ask her own questions.

"Doctor, what do these markings mean?"

He looked at her suddenly, realizing that she had no idea what she was dealing with. She was in danger and didn't even know why.

"There are these creatures called the Silence who can be seen until you turn away and then you have no memory of them. The marking on your arm was obviously from someone who has been with them before." He pointed to the markings on her wrist. At that moment he noticed the last marking curved. It was almost the shape of the crack in Amelia Pond's wall. At that moment he knew the markings on the young girl's wrist were from him; a future version, of course, trying to send a message to his younger self. He was about to ask her if she could remember if there was someone with her but knew that the girl was smart. She was hiding something from him, and wouldn't admit to him willingly the full truth; even his future self knew this. That's why he made the last line so different from the others. All he could do now is try to protect her because that's what his future self wanted. The Doctor will protect this girl until he understood the situation.

Obviously the girl meant something to the Doctor, he knew that now, but the questions became how well? Then an idea occurred to him. He began to run around the control room typing in the coordinates to someone he knew would help him understand what was going on a little better.

"Where are we going?" Emilie asked as she sat and watched him turn the different knobs.

"Time to get the Mrs." He said to her, smiling.

Emilie smiled at him, keeping up the charade, but knowing inside that this would only complicate things more.


	3. The Meeting of River Song

**Summary for the Chapter:**

> River is introduced in the story.

**Notes for the Chapter:**

> Honestly, This was one of the most confusing chapters I have ever written just because I wanted her timeline to be perfect.
> 
> Any Questions about her timeline for future reference you may ask away and I will try to answer the best I can!

The Meeting of River Song

Warning! This chapter is a bit Timey Wimey I apologize now for any confusion that may occur...

"Not again." She mumbled as she walked down the hall of the most secure prison in the galaxy. Alarms were ringing madly, as if to say Someone is escaping! But the funny thing was; the exact opposite was happening. She rolled her eyes she walked over to the phone used by the guards.

"You really need to stop sounding the alarms. I'm here now, no worries. I will be back in my cell before you even send your guards." She teased and then hung up the phone. The whirling of the alarms quickly ended as soon as a curly haired women walked into her small cell. She was River Song, notorious for murdering the one and only Doctor. She was of course also his wife; but not a whole lot of people knew that or the fact that they wedded the night she murdered him.

But of course, the story wasn't always that simple.

River Song, was forced to murder the man she loved. She was put into a 1960 Apollo Astronaut suit only to stand in the middle of Utah in a lake and shoot the one man she loved and kill him. She would then be dragged off to

Stormcage and forced to serve her twelve thousand life sentence. But as time would have it, the River Song they sent to prison out of order not already doing the act in question.

In fact, she hasn't even done it yet. This River, only just about to enter her second semester of school when she was dragged away to prison for a murder she hadn't even committed yet. River Song age 22, had no idea that she was to marry the man she loved and murder him in only 3 short years. But here she was, serving a couple lifetime prison sentence and only a couple of months into it.

At first, it was torture, until she realized that the Doctor would always be there to save her, and take her away from this nightmare he put her in. Every night, he would come crashing the Tardis by her cell and take her away somewhere magical or dangerous, just as she liked it. A couple of nights ago though, the Doctor didn't come, and River was worried. He never once missed a night, so she broke out of prison (for real this time), got a old vortex manipulator, and searched for him. In the course of those nights, River Song, Amy Pond, the Doctor and a Centurion rebooted the universe and saved it from one of the biggest threats they have ever known.

River now sat in her cell, writing down the events in her little blue diary, writing in every detail so when the day comes that the Doctor doesn't know, she won't "spoil" anything for him.

But as Ms. Song was writing away in her diary a familiar worp worp hummed from outside of her cell. She had only just left an adventure, surly he didn't need her so soon she thought as she waited for him to walk out of the old police box.

"Ah Miss River Song." The Doctor rose out of the tardis doors with a smile and leaned against the closed door.

"Oh Doctor didn't I just see you?" She flirted with him as she rose from her bed and walked over to him. Now only bars stood between them.

"That depends Miss Song, where are we?" His tone suddenly changed as he waited for her response. He could tell that River was young, which meant he knew more than her the question being how much did she know.

"I just helped you reboot the Universe. Amy and Rory married and you shocked the whole party by landing the Tardis in the middle of the dance floor."

"Ahh.." The Doctor began calculating in his mind what this meant. She hadn't yet committed the murder or know that they were married. Okay, he could work with this. He could see in her eyes that she was trying to figure out what he was hiding so he quickly changed his face to hide any concern she had.

"Well River naught of the chit chat I need you to come with me. One of your University mates contacted me and needs our help." The Doctor rambled as he used his sonic screwdriver to open River's cell.

River scrambled her mind trying to think of someone who she told details about the Doctor to but was coming up blank.

"Are they in the Tardis now?" She asked him as she watched him work on the lock.

"Ya, she had an encounter with the Silence. You do know who the Silence are right?" He suddenly worried that she wouldn't know the creatures in question.

"I have heard of them but haven't encountered them myself." Truthfully, she only knew them because they were mentioned in her trial, but besides that had no idea who or what they were.

The Doctor finally unlocked her cell door only to be startled by the alarms whirling around him. River rolled her eyes and walked over to the Tardis.

"Don't worry, they know I'll be back." She laughed as she walked into the only place she could ever truly call home. Meanwhile the Doctor stayed behind trying to stop the alarms from going off.

As River opened the Tardis doors she was startled by the presence of the young ginger girl walking around the console room not knowing who just walked in.

"Now, who might you be?" River spoke startling the girl. The girls eyes widened in shock or fear? River couldn't pinpoint it. She walked up the ramp just to get a little closer to the girl.

"Now I don't know who you are, or how you know him but I do know you lied to him about knowing me because I have no idea who you are. but I'll cover for you now just know that I have questions and I want answers." River was now almost face to face with her. The doors opened with the Doctor walking in looking a bit panicked and frazzled.

"We should get going, like now." The Doctor stated having no idea the confrontation that just happened. He looked up at the two women embracing in a hug as if they were old friends who just saw each other for the first time in a long time having no idea that it was all just an act.


	4. Looking for Answers

**Summary for the Chapter:**

> River becomes suspicious of Emilie and attempts to find out all she can about the girl.

Chapter Four: Looking for Answers

River Song kept an eye on young Emilie as the Doctor whirled around in his Tardis. Emilie pretended not to noticed Rivers stares but they were hard to ignore. Every remark the Doctor made, River would make a snide comment back about Emilie and flirt with the Doctor all at once! But of course, he was oblivious to all and continued to fly the Tardis to whatever destination he desired. This continued on for hours until finally, Emilie couldn't take it anymore.

"I'm going to go look in the Library to see if we can find any more details about the Silence." Emilie announced as she dashed out of the control room. Finally, Em could get some piece and quite without recieving glares. After walking down three different hallways Emilie finally reached the Library. The large room reminded Em of an old Earth movie "Beauty and the Beast" and just as magical. Covered from head to toe in books all categorized by planet or species with ladders everywhere to help access the different shelves. Of all the times Em had been in the Tardis she always made sure she took time to go to the library; the one room that was a constant in her life. The library was the one room in the Tardis that held the same books in anytime stream. River told her this a long time ago. So no matter when she saw the Doctor, past, present or future it would always give her the same adventures.

Emilie headed over to her favorite section, history and specifically Demon's Run. The story of Demon's Run and the Doctor was Emilie's favorite. No matter how many times she read it, she felt as though she was seeing it through new eyes. Em finally sat in the far corner making herself comfortable as she opened the book not aware that she wasn't alone anymore.

"Demon's Run huh? I don't think there is anything about the Silence." River questioned. Emilie jumped in surprise and quickly shut the book, setting it behind her.

"River. I didn't know you were in here. What can I do for you?" Emilie calmly asked trying not to show how on edge she was by River's presence. Emilie hated how much this River didn't trust her forcing Em to keep secrets she didn't normally keep.

"Well you can start by telling me exactly who you are." River took a seat in the chair next to Emilie. Em knew this question would come up eventually but she still didn't know how to answer it. Her silence filled the room as she refused to answer the question at hand. River had a feeling this would happen but what surprised her was the look in the girls eyes. It was as if she wanted to tell River the truth.

"Okay, new question then. Did you even go to the University?"

Easy. Em could be honest with this one.

"Yes; to study astronomy."

"You look young to even be in college." River remarked.

"You look to old to be with the Doctor." Em snapped. River laughed. If Ms. Song wanted to be witty then two can play that game.

"Where did you grow up?" River queried.

"Earth. In England." Emilie answered. She knew even that was too much information but she was really a horrible liar.

"Ahh young English girl. so predictable." River rolled her eyes as if it was an inside joke between her and the Doctor; she didn't know that Emilie was in on it. The Doctor and his Brits Em thought to herself before she spoke again.

"But I did my fair share of time in America as well, see my parents they liked to travel-" Emilie stopped mid sentence. She shouldn't have said that, but it just sort of slipped out. Talking about her parents and traveling was one of the major things she wasn't allowed to talk about. That was the first thing they taught her when they split up. She was so young and yet she never saw her parents together again; except for-.

"So your parents traveled? Just Earth or the Universe?"

"Both." Emilie put herself in this mess she might as well be somewhat honest now but not completely honest. The less words Em said the less River would know. River suddenly jolted up from her seat like an epiphany hit her.

"What were there names? I might have known them? Are they in trouble too?" Concern hit Rivers voice. Her attention focused again as a new angle about the girl came into River's thoughts. If she didn't know this girl, maybe she knew her parents.

Emilie stood up heading to door. These questions were becoming to much for her. Emotions were getting the best of the young girl and it was better if she just left the conversation. As her hands touched the door, Emile turned around just to say one simple, confusing word.

"Spoilers."

The Doctor was finally able to have some piece and quite. Now it was only him and the hum of the Tardis. Safe and away from the two women he turned his attention to the screen that hung about the Tardis.

Unbeknownst to River and Emilie, He took some scans of the redheaded girl hoping to gain some information. The mark left on her arm was a signal to protect her and while he was going to follow it, he wanted to know what he was getting into. The screen lit up letting him know they had the information he wanted. But the screen just left him with more questions.

**EMILIE SMITH: Species Unknown.**

He tried the search again but kept getting the same results. Emilie Smith was not human like he thought. If the Tardis didn't recognize her then that meant something was keeping him from knowing more about her. This only left him with more concerns about this girl, and why would his future self send him a message and yet not tell him what or who she is?

Deciding he needed more time to sort this out, so he went over to the control and typed in some coordinates.

"Where are we going Doctor?" Emilie bounced back up to the console room taking a seat.

"A surprise." He winked at before pulling the final switch. The ship started to sway as it was heading to its destination. The Tardis zoomed into time and space before landin. As soon as the Tardis finished landing; a Scottish voice came yelling and knocking at the front door.

"Oi! You better have my daughter in there and if you don't then take your ship and go get her!"

"Oh Pond." He laughed before opening the door to greet his old friend; Amelia Pond.


	5. The Mother Who Waited

**Summary for the Chapter:**

> Amy receives a surprise when her the Doctor and River come crashing into her backyard with a girl she has never seen before. Meanwhile the Doctor asks for her advice on what to do next with Emilie.

Chapter Five: The Mother Who Waited

Amelia Pond sat in her living room writing her traveling blog. This week was about another country she had never visited but pretended she did. It wasn't like she wasn't worldly and didn't know anything about the world, in fact she knew to much. Amelia Pond had traveled the universe in a little blue police box with her husband and imaginary friend for over few years now. Or at least she thought it was a few years; she didn't really know I mean traveling through time and space it was a bit difficult to judge how long it really was. Although, the traveling had been slowing down recently giving her time to actually get a job (the traveling blog). The last she saw of that blue box was Christmas day when he appeared on her doorstep. He only stayed for Christmas dinner and then flew away on another adventure.

It was May now, and Amy still set the table every night for four in case the Doctor showed up or time traveling daughter.

"Amy I'm home" Rory Williams (or as the Doctor called him Rory Pond) stated as he arrived home after a long day of work. After traveling, he could finally get a job as a nurse and save people the way he knew best. Rory went into the living room where Amy was writing and gave her a quick kiss before retreating up to change out of his scrubs.

Amy turned her attention back to writing until she heard the unmistakable noise of the Tardis in her backyard. She quickly ran outside just in time to see the Police Box sitting on her flowerbed, not that she minded most of the flowers were already dead.

She went to open the door only to see that the doors were locked.

"Oi! You better have my daughter in there and if you don't then take your ship and go get her!" She yelled as she knocked continuously until finally the Tardis doors opened.

"Goodness Pond aren't I good enough?" the Doctor replied before pulling her into a hug. It truly was good to have him back in her life, she missed him so much and worried about him.

"Hello Mother." River said standing directly behind the doctor and interrupted their hug. If anyone had known better, River sounded just like an annoyed teenager arriving home after a late evening.

"Would it kill you two to write every once and a while?!" Amy lectured as she led them out of the Tardis and into the backyard. Amy didn't even notice to the young girl popping from the Tardis doors.

Emilie walked out into the yard breathing in the fresh air. She of course knew who Amy was, but meeting her for the first time was, to say the least intimidating. Amy Pond was the Doctors closest friend, they sometimes knew each other better than they knew themselves and to top it all Amy is always very observant. If the Doctor couldn't solve a problem sometimes he would come to her for help which is probably why they are here. This thought freaked Emilie out more than ever. If only the Doctor could trust her and not be so curious as to know all the details.

Just as Emilie thought she could sneak by without being interrogated Amy turned around and faced the young girl.

"And who are you?" Amy was abrupt, her voice even sounding a little threatening. Everyone in the yard got silent as they turned to Emilie waiting to hear her reply.

"I'm Emilie" was all she could get out. Emilie was never one to be known for being speechless but she was at a lost for words. This was probably one of the most stressful meetings she had ever been apart of. Her name though didn't satisfy Amy.

"She's a friend from the university Mom." River cut in nonchalantly. Emilie didn't expect River to save her from the wraith of her mother but was thankful nonetheless. River was trying to make the whole conversation seem unimportant and it worked. This brought Amy's attention back to her daughter but didn't let her forget the young girl.

"Well everyone come on in! We are just about to start dinner." Amy was all excited again with a pep in her voice but still kept an eye on the newcomer.

They all began to pile into the house just in time to find Rory sitting on the couch watching TV.

"Doctor! River!" Rory greeted everyone as they entered the house. He began to hug the Doctor and River but then Rory's eyes fell on Emilie. He extended his hand to her and just smiled.

"Ah, and who are you? Did the doctor just pick you up somewhere?" Rory laughed.

"Something like that." Em replied smiling back and shaking his hand. Emilie always knew that Rory would be kinder in situations like this. Having Rory here was like a sense of comfort.

Everyone began to settle like everything was normal. Small talk was shared briefly before Amy went into the kitchen to begin cooking. With Amy out of the room, everything was a little less tense for Emily, making her feel more comfortable and..well…at home.

After a few minutes though the Doctor got up from the couch. "Excuse me I'm just going to make sure Amy doesn't burn down the house."

When the Doctor entered the room, he saw Amy in the kitchen stirring something that was on the stove. This was so domestic for her. Seeing her as a housewife, cooking a dinner, but at the same time it felt so right. He just sat and stared at her for a few minutes before Amy finally turned around.

"Oh Doctor! I didn't see you there." She said with a smile.

"I just came in to see how you were doing. Making sure you don't burn anything."

"Hey!" She laughed as she hit him on the shoulder. All of time and space they have spent together and they still act like children. The laughing slowly faded and the mood suddenly shifted.

"What's really on your mind Doctor? I know you aren't here just to share a meal, so what's going on?" Amy sudden concern for her Raggedy Man was sweet.

"It's the girl Amy. She knows me and my future self knows her. He sent her to me to protect her but I don't know why."

"Is something after her?" Amy asked.

"The Silence, but this time its different than before I can tell. They want her for something but I don't know what and the Tardis is hiding information from me about her." Frustration was building in his voice. He really wanted to help this girl but he was so in the dark about who she was. Amy put her hand on his shoulders to comfort him.

"We will find out who she is okay? Clearly she is important to you but for now you just don't know why. Just relax maybe I can talk to her and find out some information." Amy, his impossible Amy Pond was always there to comfort him just when he needed it.

"Thanks Amy." The Doctor then quickly kissed her forehead before heading back in the living room.

Amy went back to cooking. She started thinking about the young girl sitting in her living room. Who was she? Why was she so important to the Doctor?


	6. Santa Claus

**Summary for the Chapter:**

> Everything is about to change

Chapter Six: Santa Claus

Amy spent the next hour cooking and thinking over what the Doctor told her. The girl was someone important in his future but who was she? The only conclusion Amy could think of was that Emilie was the new companion, her replacement. This only began to upset Amy more making her almost burn her perfect meal.

"Dinners ready." Amy finally called as she set the table in the dinning room.

The dinner Amy cooked one of her best meal. Everyone sat in silence as they ate one of the best meals. Even the Doctor received a side of fish fingers and custard. When people weren't eating there was brief conversations about everyone's life. "So River, what have you been up to?" Amy asked her daughter.

"Oh nothing just breaking in and out of Stormcage, spending my time with the Doctor. I swear, they just keep giving me a longer sentence but how much longer can you make life in prison?" River laughed.

"I really should work on getting you out of there somehow." The Doctor contemplated. He really didn't enjoy his wife spending all of her free time in prison. She deserved to be somewhere else.

"Sweetie it doesn't matter to me, as long as I spend my nights with you." River responded sweetly while giving the Doctor a quick kiss on the cheek. Rory began to groan, seeing his daughter and his wives' imaginary friend kiss was something that still disgusted him.

"Amy absolutely superb dinner I just might have to come around here more often." The Doctor joked.

"You should. I haven't seen you since Christmas. Its like you have ditched me for a better ginger." Amy remarked as she brought the dishes in the kitchen. Emilie began to get bright red. Even though dinner went smoothly it was clear Emilie was still unwelcome in Amy's book. Emilie wanted to be liked by Amy but it looked to be a bit of a challenge.

"I think I will go help Amy with the dishes" Emilie announced. This was a suicide mission but she wanted Amy to know she wasn't a threat. No one could ever replace the Ponds not even to Em but Amy didn't know that.

Amy was by the sink when Emilie came in the room scrubbing the dishes.

"You dry." Amy said clearly hearing the conversation outside.

"Okay." Emilie said in a meek voice as she moved to stand next to Amy. The silence in the room was deadly between the two making it hard to start any sort of conversation.

"So how long have you been traveling with the Doctor?" Amy finally asked a little frustrated.

"Oh um well this is my first time." Emilie lied. Lying to Amy was like lying to her mother Em thought, but Amy went along with it.

"Been to any cool planets yet?"

"No. not really. He just sort of picked me up when I was in trouble on one planet." Emilie explained.

"So what were you running from exactly?" Amy finally turned to the young girl waiting for an answer.

"The Silence I guess. I didn't really know I was just sort of running and then I ran into the Tardis. The Doctor called them the Silence but I have never heard of them." Emilie confessed. Emile realized that she forgot the reason she was in this situation in the first place. The Silence was now the reason she was traveling with someone who had no idea who she was.

"Why are the Silence after you? You are just a girl." Amy asked. To her it was the most obvious question and should receive an obvious answer but Emilie didn't know how to answer.

"I don't know and to be honest I am scared of not knowing and everywhere I look for answers I can't seem to find them." Emilie told Amy. Amy could see the fear in the young girls eyes. This girl was still a child, why would the Silence want her?

"Emilie I'm sure everything will work out just be patient. I remember the first time I was in trouble and the Doctor came to my rescue I was praying-."

"To Santa. I know." Emilie sarcastically replied not thinking of what she had just revealed.

"How did you know that?" Amy turned but before she could say another word, the Doctor came into the kitchen.

"Amy! Emilie! Come on out play Wii with us. I am loving this tennis game it reminds me of the time-"

"Okay! We are coming now!" Amy laughed leaving the dishes to do for another time. Emilie followed her out of the kitchen to join the others but not before she felt a chill in the back of her spine. Emilie turned around expecting to see someone but she didn't know what…..

Amy entered the living room and watched as her two favorite boys were playing Tennis on the Wii. River was watching from the couch laughing hysterically at the Doctors odd motions towards the TV. The round quickly came to a close crowning the Doctor wii champion.

"Yes! I win! I-" The Doctor stopped for a second and looked down at his arm. Two tally marks were placed on the inner left arm.

The Doctor began to look around the room. River was sitting behind him, Rory was next to him while Amy was across the room. Nothing looked out of the ordinary, but something was wrong.

"Amy, come over here now." The Doctor demanded.

"Doctor what is it?" River asked suddenly in panic. She reached for the gun in her back pocket sensing the danger.

"Where is Emilie?" The Doctor looked around the room one more time but she wasn't here.

"She was right behind me in the kitche-" Amy said as the Doctor headed into the kitchen only to find that she isn't there.

Panic set into the Doctor as he realized that she must have been taken. But he didn't have time to think about that.

"We have to get out of here right now. Everyone follow me." The Doctor instructed as he headed out to the Tardis. This was his worst fear. The girl he swore to protect was taken from him. Now all he could do was put some pieces together and attempt to find her.

Everyone followed the Doctor outside but when the Doctor looked up at his Tardis he stopped in his tracks.

Kovarian stood at the door of the Tardis with a smirk on her face. It was all coming together. Only

"Where is she?" The Doctor's voice was soft but he was angry.

"Oh. Look who is still alive after all this time! I thought I had programed you better than that." She said to River. River reached out her gun to shoot only to have the Doctor stop her.

"Where is she?" He repeated louder. His voice was becoming calm but the anger was bubbling up in him.

"Looking for someone Doctor?" Kovarian replied sweetly.

"Kovarian what have you done with her?" The Doctor paced closer almost at her face.

"Oh Doctor you really should keep a closer eye on your family members. You lose them left to right." Kovarian smirked.

"What are you talking about?" The Doctor remarked, confused by her statement. Kovarian widened her eyes and began to smile brighter.

"You don't know who she is do you? Oh this is Christmas." Kovarian laughed and then whisper one last thing before she disappeared.

"Go look at that ole cot and see for yourself."


	7. The Silent Song

Chapter Seven: The Silent Song

_"Go look at that ole cot and see for yourself."_

Before the Doctor could even respond, Kovarian was gone. What did she mean by look at the cot? How could the cot have anything to do with what was going on?

"Doctor, what did she say?" River asked as she put her hand on the Doctor's shoulder.

Then it hit him.

"Oh." He whispered.

The Doctor ignored River as he ran into the Tardis. What room was the cot even in? The last time he saw it was months ago when he brought it out for baby River but where did he put it? He just began running down corridor after corridor hoping to trace his steps and find the room where the little cot laid.

Amy, Rory and River where chasing after the Doctor. The anger building in him made him run faster and ignore the fact that the Pond's were behind him. He was walking in a maze throughout the Tardis that was becoming challenging to follow.

"Where are you going?" Amy finally shouted at him. She was getting annoyed and frustrated. She wanted to know what was going on. One minute this girl anyone barely knew was on her doorstep and the next she was taken. What was the big deal?

"She told me to look at the cot. My cot the one I brought out for River when she was born but why? What would she know about that?" The Doctor just started talking to himself before he finally came across the door. He just knew this would be the room where he had put it last, it just had to be. As he opened the door he looked around at all the things he kept but wished he forgotten. The old magnified glass Donna used, Amy's little papier-mâché Tardis, Rose Tyler's jacket until his eyes finally found the Cot. Everyone else arrived in the room and began to look around at all the different things he collected over the years.

"I didn't even know this room existed." Amy baffled as she began to see all the things from companions past.

"I try to keep it hidden, to much sorrow." The Doctor replied but not really focusing on the conversation. He began to look around the little bed hoping to find some sort of answer.

"What are you looking for?" River asked as she walked closer to the Doctor.

"A name."

"Whose?"

Emilie He thought to himself. It was crazy though. He would know if she were family but at the same time how could he? The thought never crossed his mind once and even when he scanned her nothing came up. That alone should have told the him that the girl wasn't human.

Finally the Doctor found a name. Just at the head in front of his own, a name he had never seen before.

_**Freya Amelia Song** _

"Freya." The Doctor mumbled to himself. He had never heard of a Freya in his life. No one he knew in his family had that name..unless..

"Freya. Her name is Freya." The Doctor whispered closing his eyes. His hand touched the delicate Gallifreyan symbol that etched out the name. Behind him River gasped as she read the name to herself. River was putting the pieces in her head together.

"Gallifrey. We named her after Gallifrey." River stated.

"But why Emilie?" The Doctor asked River trying to understand the missing pieces.

"It's like a nickname for Amelia. She was going by her middle name." River said simply.

"Of course. Emilie Smith. She used my alias last name." The Doctor concluded. He should have known, the signs were all there.

"What are you two talking about?" Amy asked impatiently, crossing her arms. She didn't understand why the room suddenly became so silent. The Doctor just turned around and began to explain everything.

"Amelia, I don't know if I ever told you but this cot is a family heirloom of mine. It has been passed down from generation after generation until it was handed to me. Just like this Tardis, it lives in all time and space. If someone is born and placed into this cot there name would forever be etched upon it. Of course there is a bit of a catch. The name wont appear unless you have been present in the time stream."

"I don't understand." Amy stated.

"Well lets just say you went back in time before you were born and met your great-grandmother. She would know that you were her great-grandchild by looking at this cot and seeing your name etched on it. It would tell her you were family and not a threat."

"Okay, but what does this have to do with Emilie?"

"Oh it has everything to do with Emilie, Pond. See Emilie was a smart girl; she knew how to keep a secret and hide her identity was the most important one. She was probably taught at a young age to never reveal who she truly was if no one needed to know. Her one flaw though, was an old family cot that would reveal her true identity."

"Oh my god." Amy's eyes widened. She figured it out.

"That's right Pond. You're a grandma and she's your granddaughter."

Emilie opened her eyes slowly to bright lights surrounding her. Everything was white as if she was in a hospital room. She felt heavy, like a weight was being pushed down on her body. Her eyes just wanted to shut, and go back to sleep but she knew she was in danger. Drugs weren't going to keep her down for long. She would get out of here even if she ran the whole way. Emilie attempted to get up only to notice that she was tied down to the medical chair. Panic rose began to rise as she realized this was worse than she thought. Suddenly becoming more alert she saw that there were solders standing guard at the door. Emilie was trapped, with no way to escape.

"Where am I?!" She attempted to ask one of the guards but no one answered.

"What's going on?! Let me out of this chair!" Emilie screamed as she was fighting against her bonds.

"Ah. I see our little Time Lord is awake."

Emilie looked up to see that a women had entered the room with a smile across her face.

**Notes for the Chapter:**

> Freya Amelia Song. I would like to take this moment to now officially thank obsessedsoul! I read a story of her's where the Doctor and River had a child and named her Freya after Gallifrey and it just hit me. If they every had a girl that would be her name which also inspired me to write my own "Time Baby" fic. So I am using the name, but my Freya is VERY different from hers. Please if you get a chance go over and read her stories! They are just great!
> 
> Of course! Now chapter is complete without a preview and COMMENT! Please! Tell me what you think! I might even reply!
> 
> Chapter Eight: Freya Amelia Song
> 
> "Freya Amelia Song. The last daughter of Gallefrey. I have been waiting for this moment for a long time." Kovarian spoke as she paced around the room like a predator stalking its prey.
> 
> "It's Emilie."
> 
> "Of course Emilie." Kovarian mocked. "The name you told your dear old Mom and Dad who have no idea to who you truly are, do they?"
> 
> ...Just wait. I hope I can surprise you some more...


	8. Freya Amelia Song

Chapter Eight: Freya Amelia Song

Emilie looked at the women across the room; staring at the women with the eye patch across her eye. Fear should have struck her, but instead she began to remember something from her childhood.

_The day River and Freya took a trip to visit her grandparents for the first time. Amy and Rory were just settling into there new lives in New York (1940) when River stopped by to see how the "Melody Malone" story was going and to catch up. During the visit, River brought a present for her parents._

_"Here. The Doctor wanted you to have this." River handed Amy a blue photo album filled with all the photos from the future. Amy spent the afternoon reminiscing and looking though the photos with Freya._

_"This is when your granddad was a Roman. He stood by my box and waited for me 2,000 years!" Amy explained while Freya just looked wide-eyed._

_"Wow..Granddad is a superhero."_

_Amy and River laughed at the young girl. If only she could have been there River thought to herself._

_"Your father thought so too." River kissed her daughter on the head. Freya was beginning to get tired and River noticed. So she grabbed her young daughter and said good night and carried her back to her Tardis._

_While River was tucking Freya in that night though, Freya had one more question._

_"Momma, why don't Nan and Granddad have pictures of you?" A young girl asked sleepily._

_River sighed. "Its because Nan and Granddad didn't raise me. I was taken from them when I was born by a women with an eye patch. She wanted me to kill the Doctor but I never could because of your Nan. When I was your age, I went to school with them except I didn't have curly hair like this and your Nan would tell the most fantastic stories about your father. The thing was, they didn't know who I was to them except a friend and I didn't know who they were either."_

_"Wibbily Wobbily." Freya explained_

_"Timey Wimey" River laughed and kissed her daughter on the forehead._

"Freya Amelia Song. The last daughter of Gallefrey. I have been waiting for this moment for a long time." Kovarian spoke as she paced around the room like a predator stalking its prey.

"It's Emilie."

"Of course  _Emilie._ " Kovarian mocked. "The name you told your dear old Mom and Dad who have no idea to who you truly are, do they?"

Emilie didn't say anything. She didn't want to give her the satisfaction. If she wanted to play tough, Emilie was going to play tough.

"Well I think its time we move on with the plan." Kovarian stepped back while ushering forward two guards and a nurse who was wheeling in a tray of needles and an IV.

The panic set in again for Emilie. This wasn't happening. They weren't going to control. They never could.

"You can't control me! I am not my mother I am full Time Lord! Besides, you can't make me kill my own father!" Emilie persisted and screamed as the needles were getting closer to her. Kovarian stopped in her tracks and looked at Emilie.

"Oh my dear. I learned my lesson the first time. I don't want to kill the Doctor anymore. I've moved on."

"Then what are you going to do to me?" Emilie whispered. The panic was turning into fear as she realized she didn't know what was going to happen to her.

"Oh Freya Song. You are so much more valuable than your mother ever was. See with you being a full Time Lord, you hold the key to something that I want desperately."

"What?"

"Regeneration." Kovarian whispered loud enough so the whole room could hear. "See when I realized your mother would never kill the Doctor it suddenly hit me. He can travel though time and space and change his appearance and most importantly never die. Why would I want to kill something that has the power to rule the universe when I could create it and duplicate. I could conquer planets, use different faces and no one would ever know who I truly am."

"You're insane. I cant just give up my regeneration I have to be on the brink of death." Emilie rationalized.

"Exactly Ms. Song. So we are going to bring you there until we can control it."

Before Emilie could say anything else she felt a prick on her arm and then it was dark…..

 

**Notes for the Chapter:**

> What do you think? Please let me know if you liked the flashback! It was something I added in at the last minute and I really enjoyed writing it!
> 
> Now here is the preview for the next chapter:
> 
> Chapter Nine: The History Books
> 
> "I just wished I knew. I wish I could have protected her." The Doctor began say but his wife put a finger on his mouth to quite him.
> 
> "There was nothing you could do. We tried everything." River replied.
> 
> Now, COMMENT and maybe ill be nice and post the next chapter tomorrow...

**Author's Note:**

> Now who does she think she is using 10's catchphrase?!


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